rs2238628

chr19-3152984-G-Achr19-3152984-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002068.4(GNA15):c.614+1149G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0982 in 152,116 control chromosomes in the GnomAD database, including 1,393 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.098 (1393 hom., cov: 31)
• Consequence: GNA15 NM_002068.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407

Genes affected

GNA15 (HGNC:4383): (G protein subunit alpha 15) Enables G protein-coupled receptor binding activity. Involved in positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway. Predicted to be located in plasma membrane. Predicted to be part of heterotrimeric G-protein complex. [provided by Alliance of Genome Resources, Apr 2022]

GNA15-DT (HGNC:55293): (GNA15 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GNA15	NM_002068.4	c.614+1149G>A		intron_variant		ENST00000262958.4
GNA15-DT	NR_110670.1	n.158+2034C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GNA15	ENST00000262958.4	c.614+1149G>A		intron_variant		1	NM_002068.4	P1
GNA15-DT	ENST00000587587.1	n.158+2034C>T		intron_variant, non_coding_transcript_variant		2
GNA15	ENST00000586082.1	n.575+1149G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0981 AC: 14911 AN: 151998 Hom.: 1382 Cov.: 31

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.104

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0982 AC: 14934 AN: 152116 Hom.: 1393 Cov.: 31 AF XY: 0.108 AC XY: 8056 AN XY: 74370

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.0864

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.0794

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0936 Hom.: 1392

Bravo AF: 0.105

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	10
Dann	Benign	0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2238628; hg19: chr19-3152982;